Merge for 2.11.1 release

CMakeLists.txt

@@ -147,13 +147,13 @@ if(WIN32)
   set(IMP_SWIG_LIBRARIES ${PYTHON_LIBRARIES})
 endif(WIN32)
 
-if("${PYTHON_NUMPY_INCLUDE_DIR}" MATCHES ".*NOTFOUND.*")
-  file(WRITE "${CMAKE_BINARY_DIR}/build_info/NumPy" "ok=False")
-else()
+if(${PYTHON_NUMPY_FOUND})
   set(NUMPY_INCLUDE_PATH ${PYTHON_NUMPY_INCLUDE_DIR} CACHE INTERNAL "" FORCE)
   file(WRITE "${CMAKE_BINARY_DIR}/build_info/NumPy"
        "ok=True\n"
        "includepath='${NUMPY_INCLUDE_PATH}'")
+else()
+  file(WRITE "${CMAKE_BINARY_DIR}/build_info/NumPy" "ok=False")
 endif()
 
 if(NOT DEFINED PATH_SEP)

ChangeLog.md

@@ -1,26 +1,33 @@
 ChangeLog {#changelog}
 =========
 
+# 2.11.1 - 2019-07-18 # {#changelog_2_11_1}
+- Bugfix: fix build system failures with CMake 3.12 and 3.13, and on Windows.
+- Bugfix: IMP::atom::create_clone() now always copies mass, even of particles
+  that are not atoms.
+- Bugfix: IMP::rmf::create_hierarchies() should no longer fail with
+  "The filename cannot be empty".
+
 # 2.11.0 - 2019-06-25 # {#changelog_2_11_0}
 - A number of new tutorials are now available covering a variety of topics
   from modeling complexes with IMP::pmi to writing new C++ code. See
   the [tutorial index](https://integrativemodeling.org/tutorials/) for
   more details.
 - The build system has been updated to use new CMake functionality
-  (if available) to detect Python. If you have CMake 3.12 or later, this should
+  (if available) to detect Python. If you have CMake 3.14 or later, this should
   do a much better job of handling multiple Python installations (e.g. Macs
   with Homebrew). It will default to using Python 3. To force use of Python 2,
   pass `-DUSE_PYTHON2=on` to your CMake invocation.
 - CMake files are now provided to make it straightforward to use IMP as
   a library in other programs. See
-  [the tutorial](https://integrativemodeling.org/tutorials/using_cpp/develop/)
+  [the tutorial](https://integrativemodeling.org/tutorials/using_cpp/)
   for more details.
 - CMake files are now provided to build new IMP modules outside of the IMP
   build tree (i.e. a module can be built against an IMP binary).
 - The IMP::OptionParser class has been removed. Use IMP::ArgumentParser instead.
 - The IMP::test::TempDir and IMP::test::RunInTempDir utility classes have been
   removed. Use the IMP::test::temporary_directory and
-  IMP::temporary_working_directory context managers instead.
+  IMP::test::temporary_working_directory context managers instead.
 
 # 2.10.1 - 2019-02-26 # {#changelog_2_10_1}
 - Add support for OpenCV 4.

VERSION

@@ -1 +1 @@
-2.11.0
+2.11.1

doc/manual/cmake_config.md

@@ -72,7 +72,7 @@ which control the build. For example:
 
 In order to build %IMP Python extensions, CMake needs to find the Python header
 and library files that match the `python3` or `python` binary. If using a
-recent version of CMake (3.12 or later) it should have no issues in doing so.
+recent version of CMake (3.14 or later) it should have no issues in doing so.
 However, old versions of CMake might get confused if you have multiple versions
 of Python installed (for example on a Mac with [Homebrew](https://brew.sh/)),
 and find the headers for one version and the binary for another. This can
@@ -82,7 +82,7 @@ variables.
 
 For example, on a Mac with Homebrew, where `python` is Homebrew's
 `/usr/local/bin/python`, old versions of CMake will often find Apple's Python
-headers. This can be resolved (if you cannot upgrade CMake to 3.12 or later)
+headers. This can be resolved (if you cannot upgrade CMake to 3.14 or later)
 by telling CMake where the Homebrew Python headers and library
 are, by addinng to your CMake invocation something like
 `-DPYTHON_LIBRARY=/usr/local/opt/python@2/Frameworks/Python.framework/Versions/Current/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=/usr/local/opt/python@2/Frameworks/Python.framework/Versions/Current/Headers`

doc/manual/installation.md

@@ -22,7 +22,7 @@ to see if the code is currently stable enough for your purposes.
 
 In order to build %IMP from source, you will need:
 
-- [CMake](https://cmake.org) (2.8 or later; 3.12 or later is recommended)
+- [CMake](https://cmake.org) (2.8 or later; 3.14 or later is recommended)
 - [Boost](https://www.boost.org) (1.41 or later; Boost.Iostreams must be built
   with its [zlib filter enabled](https://www.boost.org/doc/libs/1_67_0/libs/iostreams/doc/installation.html))
 - [Eigen](https://eigen.tuxfamily.org/) (3.0 or later)

doc/manual/mainpage.dox

@@ -51,6 +51,7 @@ complex might want to skip ahead to
    - [Naming and interface conventions](@ref conventions)
    - [Parallelization](@ref parallel)
    - [Using the library in other projects](@ref uselibrary)
+   - [Building modules out of tree](@ref outoftree)
 
  - [Frequently asked questions (FAQ)](@ref faq)
 

doc/manual/outoftree.md

@@ -0,0 +1,65 @@
+Building modules out of tree {#outoftree}
+============================
+
+Normally to build an %IMP module it is placed in the `modules` subdirectory
+together with the rest of the %IMP source code and then all of %IMP is
+built, as per the [installation instructions](@ref installation_source).
+However, this makes builing a module an expensive process (as the build
+system needs to check whether any part of %IMP has changed, not just the
+module itself) and it is awkward to build a module against multiple
+versions of %IMP, for example against both the latest stable release and
+a more recent nightly build.
+
+An alternative is to build one or more %IMP modules 'out of tree', treating
+them as their own [CMake](https://cmake.org/) projects in their own
+directories, and pointing them to existing %IMP installation(s) using
+%IMP's [existing CMake configuration](@ref uselibrary).
+
+## Module layout
+
+Out of tree modules can be maintained in one of two ways:
+
+  1. A top-level `modules` directory containing a number of subdirectories,
+     one per module; the name of each subdirectory is the name of the module.
+     This mimics the way %IMP itself maintains multiple modules.
+  2. All of a single module's files can be placed in the top-level directory,
+     as is done for the [PMI](https://github.com/salilab/pmi/) module. This
+     has the advantage that the module can also be cloned directly into
+     %IMP's `modules` directory and built 'in tree', as well.
+
+## CMake configuration
+
+Place the [FindIMP.cmake](https://github.com/salilab/pmi/blob/develop/tools/FindIMP.cmake)
+file into a suitable directory, say a `tools` subdirectory. This file will help
+CMake to find the %IMP installation, as [described earlier](@ref uselibrary).
+
+Make a top-level `CMakeLists.txt` file. This file
+ - Adds the `tools` directory to the CMake search path, so that CMake can
+   find %IMP;
+ - Finds the %IMP package;
+ - Uses the `imp_build_module` CMake macro, provided in %IMP's CMake
+   configuration, to build the module;
+ - For the single module case, detect an 'in tree' build and fall back to
+   using %IMP's own CMake scripts.
+
+A suitable `CMakeLists.txt` can be found in the
+[PMI repository](https://github.com/salilab/pmi/blob/develop/CMakeLists.txt) -
+all that needs to be changed is `CMAKE_MODULE_PATH` (if `FindIMP.cmake` was
+not put in the `tools` directory) and the second argument to
+`imp_build_module`, which is the module name. (If multiple modules are
+being built under the `modules` directory, this second argument should
+be omitted - the module names will match those of the subdirectories.)
+
+## Building
+
+The module can now be built like any other CMake project - i.e. make a
+build directory, and run CMake in that build directory, giving it the
+path to the module source code. (You may need to set the `IMP_DIR` variable
+to help CMake find %IMP.)
+
+## Testing and running
+
+After a successful build, the build directory will contain a
+`setup_environment.sh` script. This can be used just like that in %IMP
+itself. It will add both the out of tree module(s) and %IMP to the search
+path so that the module can be tested or used.

doc/manual/uselibrary.md

@@ -32,5 +32,10 @@ file is provided to help CMake find this %IMP configuration (using the
 command), and can be used in other CMake projects. 
 
 See also the tutorial on
-[using IMP as a C++ library](https://integrativemodeling.org/tutorials/using_cpp/develop/)
+[using IMP as a C++ library](https://integrativemodeling.org/tutorials/using_cpp/)
 for a worked example of using %IMP in a CMake project.
+
+This functionality can also be used to build an %IMP module "out of tree",
+that is to build the module by itself and link to an existing pre-built
+%IMP installation. See the [out of tree](@ref outoftree) page for more
+information.

modules/atom/include/Hierarchy.h

@@ -451,7 +451,7 @@ IMPATOMEXPORT bool get_is_heterogen(Hierarchy h);
 
 //! Clone the Hierarchy
 /** This method copies the Bond, Bonded, Atom,
-    Residue, Domain, and provenance data and the particle name to the
+    Residue, Domain, Mass, and provenance data and the particle name to the
     new copies in addition to the Hierarchy relationships.
 
     \relates Hierarchy
@@ -460,7 +460,7 @@ IMPATOMEXPORT Hierarchy create_clone(Hierarchy d);
 
 //! Clone the node in the Hierarchy
 /** This method copies the Atom,
-    Residue, Chain, Domain, and provenance data and the particle name.
+    Residue, Chain, Domain, Mass, and provenance data and the particle name.
 
     \relates Hierarchy
 */

modules/atom/include/Mass.h

@@ -25,6 +25,10 @@ class IMPATOMEXPORT Mass : public Decorator {
                                 double mass) {
     m->add_attribute(get_mass_key(), pi, mass);
   }
+  static void do_setup_particle(Model *m, ParticleIndex pi,
+                                Mass o) {
+    do_setup_particle(m, pi, o.get_mass());
+  }
 
  public:
   static bool get_is_setup(Model *m, ParticleIndex pi) {
@@ -42,6 +46,7 @@ class IMPATOMEXPORT Mass : public Decorator {
   IMP_DECORATOR_METHODS(Mass, Decorator);
   /** Add the specified mass to the particle. */
   IMP_DECORATOR_SETUP_1(Mass, Float, mass);
+  IMP_DECORATOR_SETUP_1(Mass, Mass, other);
 
   /** Get the key used to store the mass. */
   static FloatKey get_mass_key();

modules/atom/src/Hierarchy.cpp

@@ -438,6 +438,11 @@ Hierarchy clone_internal(Hierarchy d,
   if (Representation::get_is_setup(d.get_particle())) {
     nd = Representation::setup_particle(p, Representation(d.get_particle()));
   }
+  // If a particle has mass but is not an atom (e.g. a PMI bead), copy the mass
+  if (Mass::get_is_setup(d.get_particle()) &&
+      !Mass::get_is_setup(p)) {
+    Mass::setup_particle(p, Mass(d.get_particle()));
+  }
   if (core::Provenanced::get_is_setup(d.get_particle())) {
     core::Provenanced pd(d.get_particle());
     core::Provenance prov = core::create_clone(pd.get_provenance());

modules/atom/test/test_clone.py

@@ -21,6 +21,18 @@ def test_bonded(self):
         mh = None
         self.assertEqual(0, len(m.get_particle_indexes()))
 
+    def test_clone_mass(self):
+        """Test clone of particles that have mass but are not atoms"""
+        m = IMP.Model()
+        p1 = IMP.Particle(m)
+        h1 = IMP.atom.Hierarchy.setup_particle(p1)
+        m1 = IMP.atom.Mass.setup_particle(p1, 4.0)
+
+        h2 = IMP.atom.create_clone(h1)
+        self.assertTrue(IMP.atom.Mass.get_is_setup(h2))
+        m2 = IMP.atom.Mass(h2)
+        self.assertAlmostEqual(m2.get_mass(), 4.0, delta=1e-4)
+
     def test_destroy_child(self):
         """Destroy of a child should update the parent"""
         m = IMP.Model()

modules/atom/test/test_mass.py

@@ -0,0 +1,25 @@
+from __future__ import print_function
+import IMP
+import IMP.test
+import IMP.atom
+
+
+class Tests(IMP.test.TestCase):
+
+    def test_mass(self):
+        """Check Mass decorator"""
+        m = IMP.Model()
+        p1 = IMP.Particle(m)
+        p2 = IMP.Particle(m)
+        # Set up using mass value
+        m1 = IMP.atom.Mass.setup_particle(p1, 1.0)
+        self.assertAlmostEqual(m1.get_mass(), 1.0, delta=1e-4)
+        m1.set_mass(2.0)
+        self.assertAlmostEqual(m1.get_mass(), 2.0, delta=1e-4)
+        # Set up using other particle
+        m2 = IMP.atom.Mass.setup_particle(p2, m1)
+        self.assertAlmostEqual(m2.get_mass(), 2.0, delta=1e-4)
+
+
+if __name__ == '__main__':
+    IMP.test.main()

modules/rmf/dependency/RMF/cmake_modules/IMPFindPython.cmake

@@ -1,8 +1,8 @@
 # Like cmake's FindPython but allows the user to override; should also
 # work (to some degree) with older cmake
 function(imp_find_python)
-  if (${CMAKE_VERSION} VERSION_LESS "3.12.0")
-    message(WARNING "Using old Python detection logic. Recommended to upgrade to cmake 3.12.0 or later")
+  if (${CMAKE_VERSION} VERSION_LESS "3.14.0")
+    message(WARNING "Using old Python detection logic. Recommended to upgrade to cmake 3.14.0 or later")
     if(NOT DEFINED PYTHON_INCLUDE_DIRS)
       execute_process(COMMAND python -c "import sys; print(sys.executable)"
                       WORKING_DIRECTORY ${PROJECT_BINARY_DIR}

modules/rmf/dependency/RMF/src/internal/paths.cpp

@@ -64,7 +64,7 @@ size_t count_path_components(boost::filesystem::path p) {
 // Remove extraneous . and .. entries from the path
 boost::filesystem::path normalize(const boost::filesystem::path& p) {
   size_t comp = count_path_components(p);
-  std::vector<bool> keep(true, comp);
+  std::vector<bool> keep(comp, true);
 
   size_t i = 0;
   for (boost::filesystem::path::iterator it(p.begin()), it_end(p.end());

tools/build/setup_cmake.py

@@ -157,14 +157,14 @@ def setup_module(finder, module, tools_dir, extra_include, extra_swig,
                                tools.to_cmake_path(x) for x in checks]))
         contents.append(
             "add_subdirectory(${CMAKE_SOURCE_DIR}/%s/compiler)" %
-            module.path)
+            tools.to_cmake_path(module.path))
     if len(deps) > 0:
         g.write(os.path.join(module.path, 'dependency', 'CMakeLists.txt'),
                 "\n".join(["include(${CMAKE_SOURCE_DIR}/%s)" %
                                tools.to_cmake_path(x) for x in deps]))
         contents.append(
             "add_subdirectory(${CMAKE_SOURCE_DIR}/%s/dependency)" %
-            module.path)
+            tools.to_cmake_path(module.path))
     local = os.path.join(module.path, "Setup.cmake")
     if os.path.exists(local):
         contents.append("include(${CMAKE_SOURCE_DIR}/%s)"
@@ -238,7 +238,7 @@ def setup_module(finder, module, tools_dir, extra_include, extra_swig,
     benchmark_template.write(benchmark, values)
     examples_template.write(examples, values)
     values["tests"] = "\n".join(contents)
-    topdir = '/' + module.path if module.path else ''
+    topdir = '/' + tools.to_cmake_path(module.path) if module.path else ''
     if finder.external_dir:
         values["build_dir"] = "--build_dir=%s " % finder.external_dir
     else:

tools/rpm/IMP.spec.in

@@ -487,6 +487,9 @@ find ${RPM_BUILD_ROOT}%{_prefix}/share/IMP/tools -name '*.py' -exec perl -pi -e
 %endif
 
 %changelog
+* Thu Jul 18 2019 Ben Webb <[email protected]>   2.11.1-1
+- 2.11.1 release.
+
 * Tue Jun 25 2019 Ben Webb <[email protected]>   2.11.0-1
 - 2.11.0 release.